X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.1
Temperature 293.0
Details mixing 6ul [5.8mg/ml Wind in 5mM HEPES pH7.5, 25mM NaCl, 0.0025%(V/V) beta-mercaptoethanol] with 3ul [0.1M MES pH6.1, 0.1M CsCl, 2mM CaCl2, 16%(V/V) PEG 300] cryo-condition: 0.1M Mes pH6.1, 20%(V/V) PEG 300, 10%(V/V)glycerol, 0.1M CsCl, 2mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.68 α = 90
b = 50.36 β = 112.84
c = 98.62 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH bent mirror 2002-07-31
Diffraction Radiation
Monochromator Protocol
Triangular monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.811 EMBL/DESY, Hamburg X11

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.9 37.64 99.8 -- 0.0565 -- 4.5 38218 38218 -- -3.0 49.18
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.9 2.0 99.6 -- 0.2759 4.77 3.79 5373

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SIRAS 1.9 35.17 -- 0.0 38216 38216 1859 99.8 0.2179 0.2179 0.21584 0.25571 5%,THIN SHELLS
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.9 1.949 2774 97 2677 0.246 0.338 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model individual isotropic B values
Mean Isotropic B 37.247
Anisotropic B[1][1] 0.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.42
Anisotropic B[2][2] -0.56
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.13
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.237
r_gen_planes_refined 0.01
r_dihedral_angle_1_deg 6.619
r_bond_refined_d 0.023
r_xyhbond_nbd_refined 0.159
r_angle_refined_deg 2.132
r_chiral_restr 0.156
r_mcbond_it 2.921
r_mcangle_it 4.579
r_scbond_it 5.91
r_symmetry_hbond_refined 0.23
r_scangle_it 8.304
r_symmetry_vdw_refined 0.202
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.163
Luzzati ESD (R-Free Set) 0.152
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3295
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 152

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.19
MAR345 data collection
SCALEPACK data scaling
XPREP data reduction
CCP4 data scaling
SHELXD phasing
SHELXE model building